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Genetic architecture of subspecies divergence in trace mineral accumulation and elemental correlations in the rice grain

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Abstract

Key message

Genome differentiation has shaped the divergence in element concentration between rice subspecies and contributed to the correlation among trace minerals in the rice grain.

Abstract

The balance between trace minerals in rice, a staple food for more than half of the world’s population, is crucial for human health. However, the genetic basis underlying the correlation between trace minerals has not been fully elucidated. To address this issue, we first quantified the concentrations of 11 trace minerals in the grains of a diversity panel of 575 rice cultivars. We found that eight elements were accumulated at significantly different levels between the indica and japonica subspecies, and we also observed significant correlation patterns among a number of elements. Further, using a genome-wide association study, we identified a total of 96 significant association loci (SALs). The differentiation of the major-effect SALs along with the different number of high-concentration alleles present in the two subspecies shaped the different element performance in indica and japonica varieties. Only a few SALs located in clusters and the majority of SALs showed subspecies/subgroup differentiation, indicating that the correlations between elements in the diversity panel were mainly caused by genome differentiation instead of shared genetic basis. The genetic architecture unveiled in this study will facilitate improvement in breeding for trace mineral content.

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Acknowledgements

This work was jointly supported by the National Key Research and Development Plan (2017YFD0800901), the National Natural Science Foundation of China (31470443 and 31501391) and the Key Research Program of the Chinese Academy of Sciences (KFZD-SW-111).

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Authors and Affiliations

  1. Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China

    Yongjun Tan, Liang Sun, Donghai Mao, Jieqiang Zhou, Youru Jiang, Jiurong Wang, Qihong Zhu, Daoyou Huang & Caiyan Chen

  2. National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China

    Qingnan Song & Han Xiao

  3. University of Toronto, Toronto, M5S2E5, Canada

    Tony Fan

  4. University of Chinese Academy of Science, Beijing, 100049, China

    Yongjun Tan & Qingnan Song

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  1. Yongjun Tan
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Contributions

CC and HX designed the research; YT and QS performed the genotyping; YT, LS, JZ, YJ, and JW performed the field experiments and elements concentration determination; YT, DM, LS, CC, QZ, and DH analyzed the data; YT, CC, DM, and TF wrote the paper. All the authors read and approved the manuscript.

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Correspondence to Caiyan Chen.

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Communicated by Albrecht E. Melchinger.

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Tan, Y., Sun, L., Song, Q. et al. Genetic architecture of subspecies divergence in trace mineral accumulation and elemental correlations in the rice grain. Theor Appl Genet 133, 529–545 (2020). https://doi.org/10.1007/s00122-019-03485-z

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